Comment[ArrayExpressAccession] E-GEOD-15709 Investigation Title Expression and metylation data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines Comment[Submitted Name] Expression and metylation data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines Publication Title Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer. Publication Author List Li M, Balch C, Montgomery JS, Jeong M, Chung JH, Yan P, Huang TH, Kim S, Nephew KP Publication DOI PubMed ID 19505326 Experimental Design methylation profiling by array transcription profiling by array Experimental Design Term Source REF EFO EFO Public Release Date 2009-04-17 Experiment Description This SuperSeries is composed of the following subset Series: GSE15372: Expression data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines. GSE15373: Promoter CpG island methylation data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines. Refer to individual Series Date of Experiment Term Source Name EFO Term Source Version Term Source File Person Last Name Li Li Balch Montgomery Jeong Chung Yan Huang Kim Nephew Person First Name Meng Meng Curt John Mikyoung JaeHoon Pearlly Tim Sun Kenneth Person Mid Initials S P Person Email menli@indiana.edu Person Affiliation Indiana University Person Phone Person Fax Person Address Medical Sciences, Indiana University, 1001 E 3rd Street, Bloomington, IN, USA Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE15709-11 P-GSE15709-10 P-GSE15709-6 P-GSE15709-4 P-GSE15709-2 P-GSE15709-7 P-GSE15709-1 P-GSE15709-5 P-GSE15709-3 P-GSE15709-9 P-GSE15709-8 P-GSE15709-21 P-GSE15709-16 P-GSE15709-15 P-GSE15709-20 P-GSE15709-18 P-GSE15709-13 P-GSE15709-12 P-GSE15709-14 P-GSE15709-19 P-GSE15709-22 P-GSE15709-17 Protocol Description ID_REF =
VALUE = normalized log2 ratio (Cy5/Cy3) representing test/reference ID_REF =
VALUE = MAS5.0 signal intensity
KN04H010_Detection =
KN04H010_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H006_Detection =
KN04H006_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H004_Detection =
KN04H004_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H002_Detection =
KN04H002_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H007_Detection =
KN04H007_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H001_Detection =
KN04H001_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H005_Detection =
KN04H005_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H003_Detection =
KN04H003_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H009_Detection =
KN04H009_Detection p-value = ID_REF =
VALUE = MAS5.0 signal intensity
KN04H008_Detection =
KN04H008_Detection p-value = Scanned on Axon GenePix 4200A scanner (Molecular Devices, Sunnyvale, CA) GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Followed Agilent protocol. Genomic DNA was isolated from parental (drug-sensitive) A2780, Round1, Round3, and Round5 cells using Qiagen DNeasy purification kits (Valencia, CA) Trizol extraction of total RNA was performed according to the manufacturer's instructions. Cells were maintained in RPMI 1640 media with 2 mM L-glutamine, 50 U/ml penicillin, 50 mg/ml streptomycin, and 10% fetal bovine serum, at 30o C Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Labeled the fluorophores Cy3 (parental A2780) or Cy5 (A2780 following various “rounds” of cisplatin treatment) following Agilent protocols LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Data were processed using R program. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed median target intensity of each array was arbitrarily set to 1000. Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation image_aquisition image_aquisition hybridization hybridization nucleic_acid_extraction nucleic_acid_extraction grow labeling labeling feature_extraction feature_extraction Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name CELL LINE Experimental Factor Type cell line Experimental Factor Term Source REF Experimental Factor Term Accession Number Comment[SecondaryAccession] GSE15709 Comment[GEOLastUpdateDate] 2009-07-16 Comment[GEOReleaseDate] 2009-04-16 Comment[ArrayExpressSubmissionDate] 2009-04-15 SDRF File E-GEOD-15709.sdrf.txt